[BioRuby] Bio-projects comparison

[Moses M. Hohman]

Hi Pjotr,

That sounds like a good plan. Along these lines . . . I had an idea  
the other day, and I'm not sure how exactly it would work, but I  
thought I'd throw it out there. One thing that bothers me about the  
open bio software libraries is that they are all or nothing. That is,  
you can download and install all of the pieces of bioperl or bioruby,  
or install none of them.

If I just needed sequence manipulation, I would still have to install  
the parts of bioruby that handle graphs, parsing pubmed entries, etc.  
This becomes problematic mostly because I might want some parts of a  
given open bio project and not others. I might want the sequence  
manipulation stuff, but might want to be able to have a choice among  
various restriction site computation libraries (as a random example).  
Even more tricky, I might be happy with the bioruby restriction site  
library but want different sequence manipulation functionality.  
However, for all of the open bio projects, it seems like whatever  
happens to be the first acceptable solution to a problem remains part  
of the software forever.

It would be much nicer if I could just install the sequence  
manipulation bioruby gem, and then install my restriction site gem of  
choice, or vice versa. And because rubygems can declare their  
dependencies, all I would have to know is that I wanted to install a  
particular restriction site library, and the basic sequence  
manipulation stuff it depended on would be autoinstalled. The  
opposite direction would be more complicated, but I'm pretty sure we  
could figure this out, and I think Ruby offers us particular power  
and flexibility for doing this over other dynamic languages. I think  
this kind of approach could eventually make bioruby a much more  
useful tool.

I don't know, what do folks think? Worth it/not worth it? Too complex?

Moses

On Jul 23, 2006, at 5:02 AM, Pjotr Prins wrote:

> Hi,
>
> I have started a comparison of BioRuby, Bioperl, Biopython and
> Bioconductor at:
>
> http://sciruby.codeforpeople.com/sr.cgi/BioProjects
>
> If you are aware of functional differences between these tool sets
> please send me an E-mail. I hope it becomes a valuable resource for
> bio-informaticians looking to solve a problem.
>
> Pj.
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> BioRuby at lists.open-bio.org
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>